What is it?

NSF definition from Goodman et al (Science 2016): Reproducibility refers to the ability of a researcher to duplicate the results of a prior study using the same materials as were used by the original investigator.

Do we agree?

Perhaps we should be talking about “Methods Reproducibility”

It is not the truth, or even an approximation of truth Reproducing the same bias/mistake = same (wrong) results

Reproducible Research

If most researchers think this is important,
why are we not working reproducibly?

What are the obstacles?

Think-Pair-Share (5 min)
http://www.socrative.com 1 Student login, Room Name :AHREN

Fritiof Nilsson Piraten

Fritiof Nilsson Piraten

Translation

Procrastination

*I will add a picture for this later…

Procrastination

How is your work affected by procrastination? (5 min) > http://www.socrative.com 2 & 3
> Student login, Room Name :AHREN

Fear

F: Fusion - Fusing the topic with bad thoughts about failure:
“I can not do this”
“It is too hard”
“It will take me too long time”

fEar

E: Excessive Goals - We get excited and want to change everything immediately
This leads to to unrealistic expectations and a high risk of failure!
Hard to keep up long term

feAr

A: Avoidance of Discomfort - All types of change will feel uncomfortable and unfamiliar at first
Avoiding discomfort, taking the easy way out (=no change)
Change is scary!

feaR

R: Remoteness from Values - Easy to loose goal and purpose
“Why am I even doing this?”

Can we overcome procrastination?

Note: Get organised! does not help!

How did the comments in Socrative fit with FEAR acronym?

My thoughts on Data management

• Acknowledge the procrastination psychology
  
• Set realistic goals but do set them
  
• A small step forward is progress!
  
• Set deadline
  
• Share and help each other & give positive feedback (e.g. github repo)
  
• 

What I aim to cover

• File names
• Project and File structure
• Version control
• Dos & Don’ts

Possibly discuss (if time allows and you are interested)

Note: I am not expert in all these topics

• Backups
  
• Programming tips
  
• Containers
  
• Workflows and pipelines

File names

• Use extentions to guide you (.txt .csv .fastq)
• Name files so that it is easy to understand and describe where it comes from (AT1_R1_trimmed.fq)
• Avoid any label that implies order relative to other files (Final1.txt UltraFinal.txt This_is_my_Final_Final_version2.txt)

File names

Project and File structure

Time: 10 minutes plus time for sharing

• Make a mind map to visualise the process of one of your projects.
  Be as detailed as you can regarding files needed and produced. Is external data required?

• How would you like to structure this project? Draw a management plan on a new piece of paper.
  Include files, folder structure, project structure and external resources required

• Put the two pieces of paper up for viewing by others.

My take on a strategy

• Totally fine if you have another strategy,
  but remember that chaos does not count as a strategy!!

Project

• Good descriptive name of project, e.g ArcticMetatranscriptome
  

• Include information about the goal and reasoning for the project README

• Data
  
• Analysis
  
• Docs
  
• Scripts
  

• Progs

Data

Read-only, raw data and meta data
This is an exact COPY of the data at the start of the project

Docs

Put documentation (e.g Rmarkdown, Notes etc)

Scripts

Scripts, such as sbatch, bash, R scripts etc

Progs

Store software installed locally, also keep source code

Analysis

Make a separate folder for each of the steps in the analysis I like to number them to get a nice order

Suggested reading:

• Ten simple rules for Reproducible Computational Research (Sandve et al, 2013)

So you have a Project and File structure

Now what?

Git & Github

What is Git?
Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

What is GitHub?
GitHub is a web page were git repositories can be shared. It is a essentially social platform for code. Good for most things that fit with Git.

Git is distributed

Useful links

https://jennybc.github.io/2014-05-12-ubc/ubc-r/session03_git.html

Basic git workflow

Shortlist of the most useful terms in git

stage (add)
commit
push

pull
clone
branch

Github Setup

Sign up to Github https://github.com/

Create a new Github repo for this workhop
Give the repo the name of your project

Check the box initialize this repository with a README

RStudio project

• File-> New Project -> Version Control -> Git
  Paste in the git hyperlink found on the github repo page under Clone or download-> SSH

• Update your project and file structure based on the discussions from your peers. Save the changes, click the Git tab on the top right window -> commit -> push
  

Alternatively you can do it from RStudio (let not bother for now)

• Start RStudio and make a new project, make sure that the check box for git is checked
  >File -> New Project -> New Directory -> Empty Project

Make directories in the Rstudio project

• Create a directory structure using your favourite system:

• In your graphical interface (Finder for Mac, Explorer for Windows)
  
• mkdir in terminal (BTW, this can be done inside of RStudio as well)

Share your repo

In Github repo: -> Settings -> Collaborators -> Search by email of Github username

Recommendations

• Commit on a regular basis, ideally when one set of work has been performed and tested.
• Write short descriptive comments to each commit

How to succeed?

Think-Pair-Share
http://www.socrative.com 4 Student login, Room Name :AHREN

It is all about you!

• Find ways that work for you and stick to them
• Recognise your favourite excuse _ Resist the temptation of procrastination
  
• Move in small steps
  
• Set goals that are realistic

Use peer pressure (in a positive way)

• Share github repos!
• Meet and discuss your research projects
• Be the spearhead of change in your respective groups!

Conquer the FEAR!